Result, in folder mutidex_source1, there are classes.dex, and classes2.dex, this is correct result
2. Compile the mutidex_source1 into apk
Java.exe -jar apktool.jar b C:\mutidex_source1 -o c:\mutidex_source1.zip
open the result mutidex_source1.zip, inside there is only classes.dex. classes2.dex file is missing.